1
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Siegl A, Afjehi-Sadat L, Wienkoop S. Systemic long-distance sulfur transport and its role in symbiotic root nodule protein turnover. JOURNAL OF PLANT PHYSIOLOGY 2024; 297:154260. [PMID: 38701679 DOI: 10.1016/j.jplph.2024.154260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/15/2024] [Accepted: 04/25/2024] [Indexed: 05/05/2024]
Abstract
Sulfur is an essential nutrient for all plants, but also crucial for the nitrogen fixing symbiosis between legumes and rhizobia. Sulfur limitation can hamper nodule development and functioning. Until now, it remained unclear whether sulfate uptake into nodules is local or mainly systemic via the roots, and if long-distance transport from shoots to roots and into nodules occurs. Therefore, this work investigates the systemic regulation of sulfur transportation in the model legume Lotus japonicus by applying stable isotope labeling to a split-root system. Metabolite and protein extraction together with mass spectrometry analyses were conducted to determine the plants molecular phenotype and relative isotope protein abundances. Data show that treatments of varying sulfate concentrations including the absence of sulfate on one side of a nodulated root was not affecting nodule development as long as the other side of the root system was provided with sufficient sulfate. Concentrations of shoot metabolites did not indicate a significant stress response caused by a lack of sulfur. Further, we did not observe any quantitative changes in proteins involved in biological nitrogen fixation in response to the different sulfate treatments. Relative isotope abundance of 34S confirmed a long-distance transport of sulfur from one side of the roots to the other side and into the nodules. Altogether, these results provide evidence for a systemic long-distance transport of sulfur via the upper part of the plant to the nodules suggesting a demand driven sulfur distribution for the maintenance of symbiotic N-fixation.
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Affiliation(s)
- Alina Siegl
- Plant-Microsymbiont Interaction Lab, Division of Molecular Systems Biology, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria; Research Support Facilities, Mass Spectrometry Unit UBB, University of Vienna, Vienna, Austria
| | - Leila Afjehi-Sadat
- Research Support Facilities, Mass Spectrometry Unit UBB, University of Vienna, Vienna, Austria
| | - Stefanie Wienkoop
- Plant-Microsymbiont Interaction Lab, Division of Molecular Systems Biology, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.
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2
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Hernandez JS, Dziubek D, Schröder L, Seydel C, Kitashova A, Brodsky V, Nägele T. Natural variation of temperature acclimation of Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2023; 175:e14106. [PMID: 38148233 DOI: 10.1111/ppl.14106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/28/2023]
Abstract
Acclimation is a multigenic trait by which plants adjust photosynthesis and metabolism to cope with a changing environment. Here, natural variations of photosynthetic efficiency and acclimation of the central carbohydrate metabolism were analyzed in response to low and elevated temperatures. For this, 18 natural accessions of Arabidopsis thaliana, originating from Cape Verde Islands and Europe, were grown at 22°C before being exposed to 4°C and 34°C for cold and heat acclimation, respectively. Absolute amounts of carbohydrates were quantified together with their subcellular distribution across plastids, cytosol and vacuole. Linear electron transport rates (ETRs) were determined together with the maximum quantum efficiency of photosystem II (Fv/Fm) for all growth conditions and under temperature fluctuation. Under elevated temperature, ETR residuals under increasing photosynthetic photon flux densities significantly correlated with the degree of temperature fluctuation at the original habitat of accessions, indicating a geographical east/west gradient of photosynthetic acclimation capacities. Plastidial sucrose concentrations positively correlated with maximal ETRs under fluctuating temperature, indicating a stabilizing role within the chloroplast. Our findings revealed specific subcellular carbohydrate distributions that contribute differentially to the photosynthetic efficiency of natural Arabidopsis thaliana accessions across a longitudinal gradient. This sheds light on the relevance of subcellular metabolic regulation for photosynthetic performance in a fluctuating environment and supports the physiological interpretation of naturally occurring genetic variation of temperature tolerance and acclimation.
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Affiliation(s)
- Jakob Sebastian Hernandez
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg
| | - Dejan Dziubek
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg
| | - Laura Schröder
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg
| | - Charlotte Seydel
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg
- Faculty of Biology, Plant Development, Ludwig-Maximilians-Universität München, Planegg
| | - Anastasia Kitashova
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg
| | - Vladimir Brodsky
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg
| | - Thomas Nägele
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg
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3
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Kitashova A, Brodsky V, Chaturvedi P, Pierides I, Ghatak A, Weckwerth W, Nägele T. Quantifying the impact of dynamic plant-environment interactions on metabolic regulation. JOURNAL OF PLANT PHYSIOLOGY 2023; 290:154116. [PMID: 37839392 DOI: 10.1016/j.jplph.2023.154116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/17/2023]
Abstract
A plant's genome encodes enzymes, transporters and many other proteins which constitute metabolism. Interactions of plants with their environment shape their growth, development and resilience towards adverse conditions. Although genome sequencing technologies and applications have experienced triumphantly rapid development during the last decades, enabling nowadays a fast and cheap sequencing of full genomes, prediction of metabolic phenotypes from genotype × environment interactions remains, at best, very incomplete. The main reasons are a lack of understanding of how different levels of molecular organisation depend on each other, and how they are constituted and expressed within a setup of growth conditions. Phenotypic plasticity, e.g., of the genetic model plant Arabidopsis thaliana, has provided important insights into plant-environment interactions and the resulting genotype x phenotype relationships. Here, we summarize previous and current findings about plant development in a changing environment and how this might be shaped and reflected in metabolism and its regulation. We identify current challenges in the study of plant development and metabolic regulation and provide an outlook of how methodological workflows might support the application of findings made in model systems to crops and their cultivation.
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Affiliation(s)
- Anastasia Kitashova
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
| | - Vladimir Brodsky
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
| | - Palak Chaturvedi
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Iro Pierides
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Arindam Ghatak
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria; Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Wolfram Weckwerth
- University of Vienna, Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, Djerassiplatz 1, 1030, Vienna, Austria; Vienna Metabolomics Center, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
| | - Thomas Nägele
- LMU Munich, Faculty of Biology, Plant Evolutionary Cell Biology, 82152, Planegg, Germany.
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4
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Kitashova A, Adler SO, Richter AS, Eberlein S, Dziubek D, Klipp E, Nägele T. Limitation of sucrose biosynthesis shapes carbon partitioning during plant cold acclimation. PLANT, CELL & ENVIRONMENT 2023; 46:464-478. [PMID: 36329607 DOI: 10.1111/pce.14483] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 06/16/2023]
Abstract
Cold acclimation is a multigenic process by which many plant species increase their freezing tolerance. Stabilization of photosynthesis and carbohydrate metabolism plays a crucial role in cold acclimation. To study regulation of primary and secondary metabolism during cold acclimation of Arabidopsis thaliana, metabolic mutants with deficiencies in either starch or flavonoid metabolism were exposed to 4°C. Photosynthesis was determined together with amounts of carbohydrates, anthocyanins, organic acids and enzyme activities of the central carbohydrate metabolism. Starch deficiency was found to significantly delay soluble sugar accumulation during cold acclimation, while starch overaccumulation did not affect accumulation dynamics but resulted in lower total amounts of \sucrose and glucose. Anthocyanin amounts were lowered in both starch deficient and overaccumulating mutants. Vice versa, flavonoid deficiency did not result in a changed starch amount, which suggested a unidirectional signalling link between starch and flavonoid metabolism. Mathematical modelling of carbon metabolism indicated kinetics of sucrose biosynthesis to be limiting for carbon partitioning in leaf tissue during cold exposure. Together with cold-induced dynamics of citrate, fumarate and malate amounts, this provided evidence for a central role of sucrose phosphate synthase activity in carbon partitioning between biosynthetic and dissimilatory pathways which stabilizes photosynthesis and metabolism at low temperature.
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Affiliation(s)
- Anastasia Kitashova
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Stephan O Adler
- Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Andreas S Richter
- Institute for Biosciences, Physiology of Plant Metabolism, University of Rostock, Rostock, Germany
| | - Svenja Eberlein
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Dejan Dziubek
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Edda Klipp
- Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Thomas Nägele
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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5
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Xu Y, Fu X. Reprogramming of Plant Central Metabolism in Response to Abiotic Stresses: A Metabolomics View. Int J Mol Sci 2022; 23:ijms23105716. [PMID: 35628526 PMCID: PMC9143615 DOI: 10.3390/ijms23105716] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/15/2022] [Accepted: 05/18/2022] [Indexed: 12/15/2022] Open
Abstract
Abiotic stresses rewire plant central metabolism to maintain metabolic and energy homeostasis. Metabolites involved in the plant central metabolic network serve as a hub for regulating carbon and energy metabolism under various stress conditions. In this review, we introduce recent metabolomics techniques used to investigate the dynamics of metabolic responses to abiotic stresses and analyze the trend of publications in this field. We provide an updated overview of the changing patterns in central metabolic pathways related to the metabolic responses to common stresses, including flooding, drought, cold, heat, and salinity. We extensively review the common and unique metabolic changes in central metabolism in response to major abiotic stresses. Finally, we discuss the challenges and some emerging insights in the future application of metabolomics to study plant responses to abiotic stresses.
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Affiliation(s)
- Yuan Xu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (Y.X.); (X.F.)
| | - Xinyu Fu
- Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Correspondence: (Y.X.); (X.F.)
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6
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Analysis of Global Gene Expression in Maize (Zea mays) Vegetative and Reproductive Tissues That Differ in Accumulation of Starch and Sucrose. PLANTS 2022; 11:plants11030238. [PMID: 35161219 PMCID: PMC8838981 DOI: 10.3390/plants11030238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022]
Abstract
Carbon allocation between vegetative and reproductive tissues impacts cereal grain production. Despite great agricultural importance, sink–source relationships have not been fully characterized at the early reproductive stages in maize. Here, we quantify the accumulation of non-structural carbohydrates and patterns of gene expression in the top internode of the stem and the female inflorescence of maize at the onset of grain filling (reproductive stage R1). Top internode stem and female inflorescence tissues of the Puma maize inbred line were collected at reproductive stage R1 (without pollination) and non-structural carbohydrates were quantified by spectrophotometry. The female inflorescence accumulated starch at higher levels than the top internode of the stem. Global mRNA transcript levels were then evaluated in both tissues by RNA sequencing. Gene expression analysis identified 491 genes differentially expressed between the female inflorescence and the top stem internode. Gene ontology classification of differentially expressed genes showed enrichment for sucrose synthesis, the light-dependent reactions of photosynthesis, and transmembrane transporters. Our results suggest that sugar transporters play a key role in sugar partitioning in the maize stem and reveal previously uncharacterized differences between the female inflorescence and the top internode of the stem at early reproductive stages.
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7
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Seydel C, Kitashova A, Fürtauer L, Nägele T. Temperature-induced dynamics of plant carbohydrate metabolism. PHYSIOLOGIA PLANTARUM 2022; 174:e13602. [PMID: 34802152 DOI: 10.1111/ppl.13602] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Carbohydrates are direct products of photosynthetic CO2 assimilation. Within a changing temperature regime, both photosynthesis and carbohydrate metabolism need tight regulation to prevent irreversible damage of plant tissue and to sustain energy metabolism, growth and development. Due to climate change, plants are and will be exposed to both long-term and short-term temperature changes with increasing amplitude. Particularly sudden fluctuations, which might comprise a large temperature amplitude from low to high temperature, pose a challenge for plants from the cellular to the ecosystem level. A detailed understanding of fundamental regulatory processes, which link photosynthesis and carbohydrate metabolism under such fluctuating environmental conditions, is essential for an estimate of climate change consequences. Further, understanding these processes is important for biotechnological application, breeding and engineering. Environmental light and temperature regimes are sensed by a molecular network that comprises photoreceptors and molecular components of the circadian clock. Photosynthetic efficiency and plant productivity then critically depend on enzymatic regulation and regulatory circuits connecting plant cells with their environment and re-stabilising photosynthetic efficiency and carbohydrate metabolism after temperature-induced deflection. This review summarises and integrates current knowledge about re-stabilisation of photosynthesis and carbohydrate metabolism after perturbation by changing temperature (heat and cold).
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Affiliation(s)
- Charlotte Seydel
- Faculty of Biology, Plant Development, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Anastasia Kitashova
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Lisa Fürtauer
- Institute for Biology III, Unit of Plant Molecular Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Thomas Nägele
- Faculty of Biology, Plant Evolutionary Cell Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
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8
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Cvetkovic J, Haferkamp I, Rode R, Keller I, Pommerrenig B, Trentmann O, Altensell J, Fischer-Stettler M, Eicke S, Zeeman SC, Neuhaus HE. Ectopic maltase alleviates dwarf phenotype and improves plant frost tolerance of maltose transporter mutants. PLANT PHYSIOLOGY 2021; 186:315-329. [PMID: 33650638 PMCID: PMC8154053 DOI: 10.1093/plphys/kiab082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 02/25/2021] [Indexed: 05/06/2023]
Abstract
Maltose, the major product of starch breakdown in Arabidopsis (Arabidopsis thaliana) leaves, exits the chloroplast via the maltose exporter1 MEX1. Consequently, mex1 loss-of-function plants exhibit substantial maltose accumulation, a starch-excess phenotype and a specific chlorotic phenotype during leaf development. Here, we investigated whether the introduction of an alternative metabolic route could suppress the marked developmental defects typical for mex1 loss-of-function mutants. To this end, we ectopically expressed in mex1 chloroplasts a functional maltase (MAL) from baker's yeast (Saccharomyces cerevisiae, chloroplastidial MAL [cpMAL] mutants). Remarkably, the stromal MAL activity substantially alleviates most phenotypic peculiarities typical for mex1 plants. However, the cpMAL lines contained only slightly less maltose than parental mex1 plants and their starch levels were, surprisingly, even higher. These findings point to a threshold level of maltose responsible for the marked developmental defects in mex1. While growth and flowering time were only slightly retarded, cpMAL lines exhibited a substantially improved frost tolerance, when compared to wild-types. In summary, these results demonstrate the possibility to bypass the MEX1 transporter, allow us to differentiate between possible starch-excess and maltose-excess responses, and demonstrate that stromal maltose accumulation prevents frost defects. The latter insight may be instrumental for the development of crop plants with improved frost tolerance.
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Affiliation(s)
- Jelena Cvetkovic
- Plant Physiology, University of Kaiserslautern, Erwin-Schrödinger-Str., D-67653 Kaiserslautern, Germany
| | - Ilka Haferkamp
- Plant Physiology, University of Kaiserslautern, Erwin-Schrödinger-Str., D-67653 Kaiserslautern, Germany
| | - Regina Rode
- Plant Physiology, University of Kaiserslautern, Erwin-Schrödinger-Str., D-67653 Kaiserslautern, Germany
| | - Isabel Keller
- Plant Physiology, University of Kaiserslautern, Erwin-Schrödinger-Str., D-67653 Kaiserslautern, Germany
| | - Benjamin Pommerrenig
- Plant Physiology, University of Kaiserslautern, Erwin-Schrödinger-Str., D-67653 Kaiserslautern, Germany
| | - Oliver Trentmann
- Plant Physiology, University of Kaiserslautern, Erwin-Schrödinger-Str., D-67653 Kaiserslautern, Germany
| | - Jacqueline Altensell
- Plant Physiology, University of Kaiserslautern, Erwin-Schrödinger-Str., D-67653 Kaiserslautern, Germany
| | | | - Simona Eicke
- Institute of Molecular Plant Biology, ETH Zürich, Universitätsstr. 2, 8092 Zurich, Switzerland
| | - Samuel C Zeeman
- Institute of Molecular Plant Biology, ETH Zürich, Universitätsstr. 2, 8092 Zurich, Switzerland
| | - H Ekkehard Neuhaus
- Plant Physiology, University of Kaiserslautern, Erwin-Schrödinger-Str., D-67653 Kaiserslautern, Germany
- Author for communication:
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9
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Kleine T, Nägele T, Neuhaus HE, Schmitz-Linneweber C, Fernie AR, Geigenberger P, Grimm B, Kaufmann K, Klipp E, Meurer J, Möhlmann T, Mühlhaus T, Naranjo B, Nickelsen J, Richter A, Ruwe H, Schroda M, Schwenkert S, Trentmann O, Willmund F, Zoschke R, Leister D. Acclimation in plants - the Green Hub consortium. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:23-40. [PMID: 33368770 DOI: 10.1111/tpj.15144] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 05/04/2023]
Abstract
Acclimation is the capacity to adapt to environmental changes within the lifetime of an individual. This ability allows plants to cope with the continuous variation in ambient conditions to which they are exposed as sessile organisms. Because environmental changes and extremes are becoming even more pronounced due to the current period of climate change, enhancing the efficacy of plant acclimation is a promising strategy for mitigating the consequences of global warming on crop yields. At the cellular level, the chloroplast plays a central role in many acclimation responses, acting both as a sensor of environmental change and as a target of cellular acclimation responses. In this Perspective article, we outline the activities of the Green Hub consortium funded by the German Science Foundation. The main aim of this research collaboration is to understand and strategically modify the cellular networks that mediate plant acclimation to adverse environments, employing Arabidopsis, tobacco (Nicotiana tabacum) and Chlamydomonas as model organisms. These efforts will contribute to 'smart breeding' methods designed to create crop plants with improved acclimation properties. To this end, the model oilseed crop Camelina sativa is being used to test modulators of acclimation for their potential to enhance crop yield under adverse environmental conditions. Here we highlight the current state of research on the role of gene expression, metabolism and signalling in acclimation, with a focus on chloroplast-related processes. In addition, further approaches to uncovering acclimation mechanisms derived from systems and computational biology, as well as adaptive laboratory evolution with photosynthetic microbes, are highlighted.
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Affiliation(s)
- Tatjana Kleine
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Thomas Nägele
- Plant Evolutionary Cell Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - H Ekkehard Neuhaus
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | | | - Alisdair R Fernie
- Central Metabolism, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Peter Geigenberger
- Plant Metabolism, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Bernhard Grimm
- Plant Physiology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Kerstin Kaufmann
- Plant Cell and Molecular Biology, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Edda Klipp
- Theoretical Biophysics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Jörg Meurer
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Torsten Möhlmann
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Timo Mühlhaus
- Computational Systems Biology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Belen Naranjo
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Jörg Nickelsen
- Molecular Plant Science, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Andreas Richter
- Physiology of Plant Organelles, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Hannes Ruwe
- Molecular Genetics, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, 10115, Germany
| | - Michael Schroda
- Molecular Biotechnology & Systems Biology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Serena Schwenkert
- Plant Biochemistry and Physiology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Munich, 82152, Germany
| | - Oliver Trentmann
- Plant Physiology, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Felix Willmund
- Molecular Genetics of Eukaryotes, Department of Biology, Technische Universität Kaiserslautern, Kaiserslautern, 67663, Germany
| | - Reimo Zoschke
- Translational Regulation in Plants, Max-Planck-Institut für Molekulare Pflanzenphysiologie, Potsdam-Golm, 14476, Germany
| | - Dario Leister
- Plant Molecular Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
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10
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Schneider K, Abazaj L, Niemann C, Schröder L, Nägele T. Cold acclimation has a differential effect on leaf vascular bundle structure and carbon export rates in natural Arabidopsis accessions originating from southern and northern Europe. PLANT DIRECT 2020; 4:e00251. [PMID: 32789285 PMCID: PMC7416751 DOI: 10.1002/pld3.251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/08/2020] [Accepted: 07/16/2020] [Indexed: 06/11/2023]
Abstract
Acclimation to low but non-freezing temperature represents an ecologically important process for Arabidopsis thaliana but also for many other plant species from temperate regions. Cold acclimation comprises and affects numerous molecular and physiological processes and the maintenance of sugar supply of sink tissue by photosynthetically active source tissue is essential for plant survival. Here, changes in vascular bundle (VB) structure at the leaf petiole were analysed together with sucrose exudation rates before and after cold acclimation. Six natural Arabidopsis accessions originating from southern and northern Europe were compared. Photosynthetic efficiency, that is, maximum and effective quantum yield of photosystem II, revealed a significant effect of environmental condition. Only for northern accessions was a highly significant negative correlation observed between leaf sucrose exudation rates, xylem, and petiole cross-sectional areas. Furthermore, only for northern accessions was a significant increase of VB and leaf petiole cross-sectional area observed during cold acclimation. In contrast, variance of cross-sectional areas of cold acclimated southern accessions was strongly reduced compared to control plants, while mean areas remained similar under both conditions. In summary, these findings suggest that natural Arabidopsis accessions from northern Europe significantly adjust sink strength and leaf VB structure to maintain plant growth and photosynthesis under low temperature.
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Affiliation(s)
- Katja Schneider
- Department Biology IPlant DevelopmentLMU MünchenPlanegg‐MartinsriedGermany
| | - Lorena Abazaj
- Department Biology IPlant Evolutionary Cell BiologyLMU MünchenPlanegg‐MartinsriedGermany
| | - Cornelia Niemann
- Department Biology IPlant DevelopmentLMU MünchenPlanegg‐MartinsriedGermany
| | - Laura Schröder
- Department Biology IPlant Evolutionary Cell BiologyLMU MünchenPlanegg‐MartinsriedGermany
| | - Thomas Nägele
- Department Biology IPlant Evolutionary Cell BiologyLMU MünchenPlanegg‐MartinsriedGermany
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11
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Fürtauer L, Weiszmann J, Weckwerth W, Nägele T. Dynamics of Plant Metabolism during Cold Acclimation. Int J Mol Sci 2019; 20:E5411. [PMID: 31671650 PMCID: PMC6862541 DOI: 10.3390/ijms20215411] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/26/2022] Open
Abstract
Plants have evolved strategies to tightly regulate metabolism during acclimation to a changing environment. Low temperature significantly constrains distribution, growth and yield of many temperate plant species. Exposing plants to low but non-freezing temperature induces a multigenic processes termed cold acclimation, which eventually results in an increased freezing tolerance. Cold acclimation comprises reprogramming of the transcriptome, proteome and metabolome and affects communication and signaling between subcellular organelles. Carbohydrates play a central role in this metabolic reprogramming. This review summarizes current knowledge about the role of carbohydrate metabolism in plant cold acclimation with a focus on subcellular metabolic reprogramming, its thermodynamic constraints under low temperature and mathematical modelling of metabolism.
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Affiliation(s)
- Lisa Fürtauer
- Plant Evolutionary Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Bavaria, Germany.
| | - Jakob Weiszmann
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna 1090, Austria.
- Vienna Metabolomics Center, University of Vienna, Vienna 1090, Austria.
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna 1090, Austria.
- Vienna Metabolomics Center, University of Vienna, Vienna 1090, Austria.
| | - Thomas Nägele
- Plant Evolutionary Cell Biology, Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Bavaria, Germany.
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12
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Ghatak A, Chaturvedi P, Weckwerth W. Metabolomics in Plant Stress Physiology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2019; 164:187-236. [PMID: 29470599 DOI: 10.1007/10_2017_55] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.
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Affiliation(s)
- Arindam Ghatak
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, Faculty of Sciences, University of Vienna, Vienna, Austria. .,Vienna Metabolomics Center (VIME), University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
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13
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Zhang W, Chen M, Meng HL, Yang J, Wei X, Yang SC. Molecular cloning and expression analysis of SRLK1 gene in self-incompatible Asteraceae species Erigeron breviscapus. Mol Biol Rep 2019; 46:3157-3165. [PMID: 30963357 DOI: 10.1007/s11033-019-04773-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/19/2019] [Indexed: 12/23/2022]
Abstract
Based on the transcriptome data, using RACE techniques, we cloned the full-length EbSRLK1 gene in a medicinal, self-incompatible Asteraceae species, Erigeron breviscapus. Bioinformatics approaches were used to analyze the DNA and protein sequences, physical and chemical properties, and domains of the encoded protein. The full-length EbSRLK1 cDNA is 2891 base pairs (bp) with an open reading frame (ORF) of 2634 bp, which encodes the EbSRLK1 protein with 878 amino acids and an estimated molecular weight of 98.13 kD. The EbSRLK1 protein has the characteristic domain structure of S-locus receptor-like protein kinases, which contains one transmembrane domain but lacks the signal peptide. Quantitative real-time PCR (qRT-PCR) analysis showed that the EbSRLK1 gene is lowly expressed in roots, stems and leaves, but highly expressed in flowers, especially in flowers one day prior to opening. Western blot analysis showed that the EbSRLK1 protein is expressed in stems, leaves, and flowers, but is almost undetectable in roots. The EbSRLK1 protein expression is induced in self-pollinated but not in cross-pollinated E. breviscapus flowers. Cloning and expression analysis of EbSRLK1 lay a solid foundation for elucidating the role of EbSRLK1 in regulating self-incompatibility in E. breviscapus.
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Affiliation(s)
- Wei Zhang
- Honghe University, Mengzi, 661100, Yunnan, China.
| | - Mo Chen
- National and Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwest, Yunnan Agricultural University, Kunming, 650201, Yunnan, China
| | | | - Jin Yang
- Honghe University, Mengzi, 661100, Yunnan, China
| | - Xiang Wei
- Honghe University, Mengzi, 661100, Yunnan, China
| | - Sheng-Chao Yang
- National and Local Joint Engineering Research Center on Germplasm Utilization & Innovation of Chinese Medicinal Materials in Southwest, Yunnan Agricultural University, Kunming, 650201, Yunnan, China.
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14
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Preiner J, Wienkoop S, Weckwerth W, Oburger E. Molecular Mechanisms of Tungsten Toxicity Differ for Glycine max Depending on Nitrogen Regime. FRONTIERS IN PLANT SCIENCE 2019; 10:367. [PMID: 31001297 PMCID: PMC6454624 DOI: 10.3389/fpls.2019.00367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/08/2019] [Indexed: 05/06/2023]
Abstract
Tungsten (W) finds increasing application in military, aviation and household appliance industry, opening new paths into the environment. Since W shares certain chemical properties with the essential plant micronutrient molybdenum (Mo), it is proposed to inhibit enzymatic activity of molybdoenzymes [e.g., nitrate reductase (NR)] by replacing the Mo-ion bound to the co-factor. Recent studies suggest that W, much like other heavy metals, also exerts toxicity on its own. To create a comprehensive picture of tungsten stress, this study investigated the effects of W on growth and metabolism of soybean (Glycine max), depending on plant nitrogen regime [nitrate fed (N fed) vs. symbiotic N2 fixation (N fix)] by combining plant physiological data (biomass production, starch and nutrient content, N2 fixation, nitrate reductase activity) with root and nodule proteome data. Irrespective of N regime, NR activity and total N decreased with increasing W concentrations. Nodulation and therefore also N2 fixation strongly declined at high W concentrations, particularly in N fix plants. However, N2 fixation rate (g N fixed g-1 nodule dwt) remained unaffected by increasing W concentrations. Proteomic analysis revealed a strong decline in leghemoglobin and nitrogenase precursor levels (NifD), as well as an increase in abundance of proteins involved in secondary metabolism in N fix nodules. Taken together this indicates that, in contrast to the reported direct inhibition of NR, N2 fixation appears to be indirectly inhibited by a decrease in nitrogenase synthesis due to W induced changes in nodule oxygen levels of N fix plants. Besides N metabolism, plants exhibited a strong reduction of shoot (both N regimes) and root (N fed only) biomass, an imbalance in nutrient levels and a failure of carbon metabolic pathways accompanied by an accumulation of starch at high tungsten concentrations, independent of N-regime. Proteomic data (available via ProteomeXchange with identifier PXD010877) demonstrated that the response to high W concentrations was independent of nodule functionality and dominated by several peroxidases and other general stress related proteins. Based on an evaluation of several W responsive proteotypic peptides, we identified a set of protein markers of W stress and possible targets for improved stress tolerance.
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Affiliation(s)
- Julian Preiner
- Division of Molecular Systems Biology, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | - Stefanie Wienkoop
- Division of Molecular Systems Biology, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Division of Molecular Systems Biology, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Eva Oburger
- Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
- Division of Terrestrial Ecosystem Research, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
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15
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Fürtauer L, Pschenitschnigg A, Scharkosi H, Weckwerth W, Nägele T. Combined multivariate analysis and machine learning reveals a predictive module of metabolic stress response in Arabidopsis thaliana. Mol Omics 2018; 14:437-449. [PMID: 30387490 PMCID: PMC6289107 DOI: 10.1039/c8mo00095f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/24/2018] [Indexed: 12/25/2022]
Abstract
Abiotic stress exposure of plants induces metabolic reprogramming which is tightly regulated by signalling cascades connecting transcriptional with translational and metabolic regulation. Complexity of such interconnected metabolic networks impedes the functional understanding of molecular plant stress response compromising the design of breeding strategies and biotechnological processes. Thus, defining a molecular network to enable the prediction of a plant's stress mode will improve the understanding of stress responsive biochemical regulation and will yield novel molecular targets for technological application. Arabidopsis wild type plants and two mutant lines with deficiency in sucrose or starch metabolism were grown under ambient and combined cold/high light stress conditions. Stress-induced dynamics of the primary metabolome and the proteome were quantified by mass spectrometry. Wild type data were used to train a machine learning algorithm to classify mutant lines under control and stress conditions. Multivariate analysis and classification identified a module consisting of 23 proteins enabling the reliable prediction of combined temperature/high light stress conditions. 18 of these 23 proteins displayed putative protein-protein interactions connecting transcriptional regulation with regulation of primary and secondary metabolism. The identified stress-responsive core module supports prediction of complex biochemical regulation under changing environmental conditions.
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Affiliation(s)
- Lisa Fürtauer
- Ludwig-Maximilians-Universität München
, Department Biology I
, Plant Evolutionary Cell Biology
,
Großhadernerstr. 2-4
, D-82152 Planegg-Martinsried
, Germany
.
; Fax: +49-89-2180-74661
; Tel: +49-89-2180-74660
| | - Alice Pschenitschnigg
- Department of Ecogenomics and Systems Biology
, University of Vienna
,
Vienna
, Austria
| | - Helene Scharkosi
- Department of Ecogenomics and Systems Biology
, University of Vienna
,
Vienna
, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology
, University of Vienna
,
Vienna
, Austria
- Vienna Metabolomics Center
, University of Vienna
,
Vienna
, Austria
| | - Thomas Nägele
- Ludwig-Maximilians-Universität München
, Department Biology I
, Plant Evolutionary Cell Biology
,
Großhadernerstr. 2-4
, D-82152 Planegg-Martinsried
, Germany
.
; Fax: +49-89-2180-74661
; Tel: +49-89-2180-74660
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16
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Weiszmann J, Fürtauer L, Weckwerth W, Nägele T. Vacuolar sucrose cleavage prevents limitation of cytosolic carbohydrate metabolism and stabilizes photosynthesis under abiotic stress. FEBS J 2018; 285:4082-4098. [DOI: 10.1111/febs.14656] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/22/2018] [Accepted: 09/07/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Jakob Weiszmann
- Department of Ecogenomics and Systems Biology University of Vienna Austria
- Vienna Metabolomics Center (ViMe) University of Vienna Austria
| | - Lisa Fürtauer
- Department Biology I Ludwig‐Maximilians‐Universität München Planegg‐Martinsried Germany
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology University of Vienna Austria
- Vienna Metabolomics Center (ViMe) University of Vienna Austria
| | - Thomas Nägele
- Department Biology I Ludwig‐Maximilians‐Universität München Planegg‐Martinsried Germany
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17
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Nukarinen E, Tomanov K, Ziba I, Weckwerth W, Bachmair A. Protein sumoylation and phosphorylation intersect in Arabidopsis signaling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:505-517. [PMID: 28419593 PMCID: PMC5518230 DOI: 10.1111/tpj.13575] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/08/2017] [Accepted: 04/11/2017] [Indexed: 05/09/2023]
Abstract
Conjugation of the small ubiquitin-related modifier (SUMO) to protein substrates has an impact on stress responses and on development. We analyzed the proteome and phosphoproteome of mutants in this pathway. The mutants chosen had defects in SUMO ligase SIZ1, which catalyzes attachment of single SUMO moieties onto substrates, and in ligases PIAL1 and PIAL2, which are known to form SUMO chains. A total of 2657 proteins and 550 phosphopeptides were identified and quantified. Approximately 40% of the proteins and 20% of the phosphopeptides showed differences in abundance in at least one of the analyzed genotypes, demonstrating the influence of SUMO conjugation on protein abundance and phosphorylation. The data show that PIAL1 and PIAL2 are integral parts of the SUMO conjugation system with an impact on stress response, and confirm the involvement of SIZ1 in plant defense. We find a high abundance of predicted SUMO attachment sites in phosphoproteins (70% versus 40% in the total proteome), suggesting convergence of phosphorylation and sumoylation signals onto a set of common targets.
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Affiliation(s)
- Ella Nukarinen
- Department of Ecogenomics and Systems BiologyBZAUniversity of ViennaViennaAustria
| | - Konstantin Tomanov
- Department of Biochemistry and Cell BiologyCenter for Molecular BiologyMax F. Perutz LaboratoriesViennaAustria
| | - Ionida Ziba
- Department of Biochemistry and Cell BiologyCenter for Molecular BiologyMax F. Perutz LaboratoriesViennaAustria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems BiologyBZAUniversity of ViennaViennaAustria
- Vienna Metabolomics CenterUniversity of ViennaA‐1060ViennaAustria
| | - Andreas Bachmair
- Department of Biochemistry and Cell BiologyCenter for Molecular BiologyMax F. Perutz LaboratoriesViennaAustria
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18
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Hoermiller II, Naegele T, Augustin H, Stutz S, Weckwerth W, Heyer AG. Subcellular reprogramming of metabolism during cold acclimation in Arabidopsis thaliana. PLANT, CELL & ENVIRONMENT 2017; 40:602-610. [PMID: 27642699 DOI: 10.1111/pce.12836] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/10/2016] [Indexed: 05/18/2023]
Abstract
Metabolite changes in plant leaves during exposure to low temperatures involve re-allocation of a large number of metabolites between sub-cellular compartments. Therefore, metabolite determination at the whole cell level may be insufficient for interpretation of the functional significance of cellular compounds. To investigate the cold-induced metabolite dynamics at the level of individual sub-cellular compartments, an integrative platform was developed that combines quantitative metabolite profiling by gas chromatography coupled to mass spectrometry (GC-MS) with the non-aqueous fractionation technique allowing separation of cytosol, vacuole and the plastidial compartment. Two mutants of Arabidopsis thaliana representing antipodes in the diversion of carbohydrate metabolism between sucrose and starch were compared to Col-0 wildtype before and after cold acclimation to investigate interactions of cold acclimation with subcellular re-programming of metabolism. A multivariate analysis of the data set revealed dominant effects of compartmentation on metabolite concentrations that were modulated by environmental condition and genetic determinants. While for both, the starchless mutant of plastidial phospho-gluco mutase (pgm) and a mutant defective in sucrose-phosphate synthase A1, metabolic constraints, especially at low temperature, could be uncovered based on subcellularly resolved metabolite profiles, only pgm had lowered freezing tolerance. Metabolic profiles of pgm point to redox imbalance as a possible reason for reduced cold acclimation capacity.
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Affiliation(s)
- Imke I Hoermiller
- Institute of Biomaterials and Biomolecular Systems, Department of Plant Biotechnology, University of Stuttgart, 70569, Stuttgart, Germany
| | - Thomas Naegele
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14, 1090, Vienna, Austria
| | - Hanna Augustin
- Institute of Biomaterials and Biomolecular Systems, Department of Plant Biotechnology, University of Stuttgart, 70569, Stuttgart, Germany
| | - Simon Stutz
- Institute of Biomaterials and Biomolecular Systems, Department of Plant Biotechnology, University of Stuttgart, 70569, Stuttgart, Germany
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Althanstr. 14, 1090, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14, 1090, Vienna, Austria
| | - Arnd G Heyer
- Institute of Biomaterials and Biomolecular Systems, Department of Plant Biotechnology, University of Stuttgart, 70569, Stuttgart, Germany
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19
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Liu T, Li Y, Duan W, Huang F, Hou X. Cold acclimation alters DNA methylation patterns and confers tolerance to heat and increases growth rate in Brassica rapa. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1213-1224. [PMID: 28158841 PMCID: PMC5441862 DOI: 10.1093/jxb/erw496] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Epigenetic modifications are implicated in plant adaptations to abiotic stresses. Exposure of plants to one stress can induce resistance to other stresses, a process termed cross-adaptation, which is not well understood. In this study, we aimed to unravel the epigenetic basis of elevated heat-tolerance in cold-acclimated Brassica rapa by conducting a genome-wide DNA methylation analysis of leaves from control (CK) and cold-acclimated (CA) plants. We found that both methylation and demethylation occurred during cold acclimation. Two significantly altered pathways, malate dehydrogenase activity and carbon fixation, and 1562 differentially methylated genes, including BramMDH1, BraKAT2, BraSHM4, and Bra4CL2, were identified in CA plants. Genetic validation and treatment of B. rapa with 5-aza-2-deoxycytidine (Aza) suggested that promoter demethylation of four candidate genes increased their transcriptional activities. Physiological analysis suggested that elevated heat-tolerance and high growth rate were closely related to increases in organic acids and photosynthesis, respectively. Functional analyses demonstrated that the candidate gene BramMDH1 (mMDH: mitochondrial malate dehydrogenase) directly enhances organic acids and photosynthesis to increase heat-tolerance and growth rate in Arabidopsis. However, Aza-treated B. rapa, which also has elevated BramMDH1 levels, did not exhibit enhanced heat-tolerance. We therefore suggest that DNA demethylation alone is not sufficient to increase heat-tolerance. This study demonstrates that altered DNA methylation contributes to cross-adaptation.
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Affiliation(s)
- Tongkun Liu
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ying Li
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Weike Duan
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Feiyi Huang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xilin Hou
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
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20
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Fürtauer L, Weckwerth W, Nägele T. A Benchtop Fractionation Procedure for Subcellular Analysis of the Plant Metabolome. FRONTIERS IN PLANT SCIENCE 2016; 7:1912. [PMID: 28066469 PMCID: PMC5177628 DOI: 10.3389/fpls.2016.01912] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 12/02/2016] [Indexed: 05/06/2023]
Abstract
Although compartmentation is a key feature of eukaryotic cells, biological research is frequently limited by methods allowing for the comprehensive subcellular resolution of the metabolome. It has been widely accepted that such a resolution would be necessary in order to approximate cellular biochemistry and metabolic regulation, yet technical challenges still limit both the reproducible subcellular fractionation and the sample throughput being necessary for a statistically robust analysis. Here, we present a method and a detailed protocol which is based on the non-aqueous fractionation technique enabling the assignment of metabolites to their subcellular localization. The presented benchtop method aims at unraveling subcellular metabolome dynamics in a precise and statistically robust manner using a relatively small amount of tissue material. The method is based on the separation of cellular fractions via density gradients consisting of organic, non-aqueous solvents. By determining the relative distribution of compartment-specific marker enzymes together with metabolite profiles over the density gradient it is possible to estimate compartment-specific metabolite concentrations by correlation. To support this correlation analysis, a spreadsheet is provided executing a calculation algorithm to determine the distribution of metabolites over subcellular compartments. The calculation algorithm performs correlation of marker enzyme activity and metabolite abundance accounting for technical errors, reproducibility and the resulting error propagation. The method was developed, tested and validated in three natural accessions of Arabidopsis thaliana showing different ability to acclimate to low temperature. Particularly, amino acids were strongly shuffled between subcellular compartments in a cold-sensitive accession while a cold-tolerant accession was characterized by a stable subcellular metabolic homeostasis. Finally, we conclude that subcellular metabolome analysis is essential to unambiguously unravel regulatory strategies being involved in plant-environment interactions.
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Affiliation(s)
- Lisa Fürtauer
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
| | - Thomas Nägele
- Department of Ecogenomics and Systems Biology, University of ViennaVienna, Austria
- Vienna Metabolomics Center, University of ViennaVienna, Austria
- *Correspondence: Thomas Nägele
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